plot_index_shp: Plot rectangles colored by a quantitative attribute and...

In pliman: Tools for Plant Image Analysis

Plot rectangles colored by a quantitative attribute and overlay on an RGB image

Description

This function plots rectangles on top of an RGB image, where each rectangle is colored based on a quantitative variable. The quantitative variable is specified in the attribute argument and should be present in the object_index of the object computed using analyze_objects_shp(). The rectangles are colored using a color scale.

Usage

plot_index_shp(
  object,
  attribute = "coverage",
  color = c("red", "green"),
  viewer = c("mapview", "base"),
  max_pixels = 5e+05,
  downsample = NULL,
  downsample_fun = NULL,
  alpha = 0.5,
  legend.position = "bottom",
  na.color = "gray",
  classes = 6,
  round = 3,
  horiz = TRUE
)

Arguments

object	An object computed with analyze_objects_shp().
attribute	The name of the quantitative variable in the object_index to be used for coloring the rectangles.
color	A vector of two colors to be used for the color scale.
viewer	The viewer option. If not provided, the value is retrieved using get_pliman_viewer(). This option controls the type of viewer to use for interactive plotting. The available options are "base" and "mapview". If set to "base", the base R graphics system is used for interactive plotting. If set to "mapview", the mapview package is used. To set this argument globally for all functions in the package, you can use the set_pliman_viewer() function. For example, you can run set_pliman_viewer("mapview") to set the viewer option to "mapview" for all functions.
max_pixels	integer > 0. Maximum number of cells to plot the index. If max_pixels < npixels(img), downsampling is performed before plotting the index. Using a large number of pixels may slow down the plotting time.
downsample	integer; for each dimension the number of pixels/lines/bands etc that will be skipped; Defaults to NULL, which will find the best downsampling factor to approximate the max_pixels value.
downsample_fun	function; if given, downsampling will apply ⁠downsample_fun`` ⁠ to each of the the subtiles.
alpha	The transparency level of the rectangles' color (between 0 and 1).
legend.position	The position of the color legend, either "bottom" or "right".
na.color	The color to be used for rectangles with missing values in the quantitative variable.
classes	The number of classes in the color scale.
round	The number of decimal places to round the legend values.
horiz	Logical, whether the legend should be horizontal (TRUE) or vertical (FALSE).

Value

The function plots rectangles colored by the specified quantitative variable on top of the RGB image and shows the continuous color legend outside the plot.

Examples

if(interactive()){
library(pliman)

# Computes the DGCI index for each flax leaf
flax <- image_pliman("flax_leaves.jpg", plot =TRUE)
res <-
   analyze_objects_shp(flax,
                       buffer_x = 0.2,
                       buffer_y = 0.2,
                       nrow = 3,
                       ncol = 5,
                       plot = FALSE,
                       object_index = "DGCI")
plot(res$final_image)
plot_index_shp(res)
}

pliman documentation built on Oct. 15, 2023, 1:06 a.m.